work

R E S E A R C H

Robert Kincaid is a Senior Research Scientist in the Systems Biology Project in the Molecular Technology Laboratory at Agilent Laboratories. His main research interests are centered around user interface research to support interactive and visually-oriented data mining across combinations of widely disparate data. For in further details consult his CV/Resume.

From a computer science perspective these research interests group in roughly two categories:

1. Information Visualization and Visual Analytics - These are efforts to effectively visualize large multivariate datasets in ways that reveal insights in the data. Of course most of this data comes from Agilent life science instruments. Some examples include:

Signal Lens: A Focus+Context approach for analyzing large time series of electronic signals. SignalLens enables a very compact visualization which supports ad hoc visual data mining of long electronic time series. A brief video demo was presented by Agilent CTO Darlene Solomon at the IEEE MTT-S International Microwave Symposium in 2009. This work has been accepted for presentation at the 2010 IEEE Information Visualization Conference.

RFLP Decoder: This software was developed to support authenticating fish species; a problem important to the food industry and critical to complying with new regulations to protect endangered fish species from being overfished. This is now part of an Agilent product (Agilent DNA Fish ID Solution) and was published in the Journal of Visual Experiments. So you can see a complete demo of the lab protocol as well as the software.

MassVis: This project supported a novel proteomics workflow developed by Kurt Dejgaard at McGill University. A cleverly designed scatter plot interface provides a highly interactive information browser for discovery of putative protein complexes. Pattern similarity matching is used to match ‘‘profiles’’ of similar proteins as a predictor of membership in a protein complex. Both supervised, interactive methods are provided as well as completely unsupervised complex prediction. This work was presented at the 2009 IEEE Symposium on Visual Analytics Science and Technology.

Line Graph Explorer: A scalable Focus+Context visualization designed specifically for large collections of line graphs. This work was done with the help of Heidi Lam at the University of British Columbia. Presented at AVI 2006, Venice Italy. You can also view a video demo (~100Mb!)

LGE was also featured on Information Aesthetics.

VistaChrom: A visual environment for analyzing array-based comparative genomic hybridization data (aCGH). This was transferred as part of a new commercial aCGH platform and is now part of Agilent Genomic Workbench. See the recent publication in “Information Visualization” for details. Published in Information Visualization. [preprint]

VistaClara: An exploratory heat map style visualization of gene expression data that combines additional meta-data to assist in finding meaningful patterns and biological insight. Published in SAC 2004 Proceedings.

2. Computational Data Analysis - This is primarily concerned with low-level analysis of data from microarrays, liquid chromatography, mass spectrometry, or more recently electropherograms from the Agilent 2100 Bioanalyzer. Here is an example from Mass Spectrometry:

$hdl subfractions$
Deconvolution of HDL Subfractions: Agilent has developed an assay for measuring HDL subfractions from human serum using the Agilent Bioanalyzer microfluidic platform. This required a novel and fully automatic algorithm to fit Gaussian peak shapes to the expected fractions. This enabled deconvoluting the overlapping peaks and permitted measurements of the HDL components. This algorithm was used to measure data from real clinical samples as published in Clinical Chemistry and Laboratory Medicine (see Muller et al. 2007 below).

Mass Hunter/ Mass Profiler: A visual environment for analyzing proteomic and metabolomic biomarkers using Mass Spectrometry. This software was announced and demonstrated at ASMS 2005 and released in late 2005. I contributed the plotting graphics and user interface improvements.

Recent Publications

Robert Kincaid, SignalLens: Focus+Context Applied to Electronic Time Series, IEEE Trans. Vis. Comput. Graph. (VisWeek 2010) 16, 6 (2010) in press.

Formosa R, Ravi H, Happe S, Huffman D, Novoradovskaya N, Kincaid R, Garrett S (2010). DNA-based Fish Species Identification Protocol. JoVE. 38. http://www.jove.com/index/details.stp?id=1871, doi: 10.3791/1871

R. Kincaid, K. Dejgaard, MassVis: Visual Analysis of Protein Complexes Using Mass Spectrometry, IEEE Symposium on Visual Analytics Science and Technology (IEEE VAST ‘09), Atlantic City NJ, October 11-12 2009.

A. Barsky, T. Munzner, J. Gardy, R. Kincaid, Cerebral: Visualizing Multiple Experimental Conditions on a Graph with Biological Context, IEEE Transactions on Visualization and Computer Graphics, 2008, 14, 6 1253-1260.

R. Kincaid, A. Kuchinsky, M. Creech, VistaClara: an expression browser plug-in for Cytoscape, Bioinformatics 24, 18 (2008) 2112.

Mueller, O.; Chang, E.; Deng, D.; Franz, T.; Jing, D.; Kincaid, R.; Konigshofer, Y.; Kratzmeier, M.; McNulty, M.; Qian, H.; Schneider, J.; Schulte, H.; Seedorf, U.; Tian, X.; Cleve, M. V.; Yang, D.; Assmann, G., PROCAM Study: risk prediction for myocardial infarction using microfluidic high density lipoprotein (HDL) sub-fractionation is independent of HDL-cholesterol. Clinical Chemistry and Laboratory Medicine 2008, 46(4) 490-498.

Lam, H.; Munzner, T.; Kincaid, R., Overview use in multiple visual information resolution interfaces. IEEE Transactions on Visualization and Computer Graphics 2007, 13(6) 1278-1285.

R. Kincaid, H. Lam, Line Graph Explorer: Scalable Display of Line Graphs Using Focus+Context, Proc. of the Workshop on Advanced Visual Interfaces (AVI'06), ACM Press, Venice, Italy 2006.

D. X. Deng, A. Tsalenko, A. Vailaya, A. Ben-Dor, R. Kundu, I. Estay, R. Tabibiazar, R. Kincaid, Z. Yakhini, L. Bruhn, T. Quertermous, Differences in vascular bed disease susceptibility reflect differences in gene expression response to atherogenic stimuli, Circulation Research 98, 2 (2006) 200.

R. Kincaid, A. Ben-Dor, Z. Yakhini, Exploratory visualization of array-based comparative genomic hybridization, Information Visualization 4, 3 (2005) 176. [preprint]

J. Y. King, R. Ferrara, R. Tabibiazar, J. M. Spin, M. M. Chen, A. Kuchinsky, A. Vailaya, R. Kincaid, A. Tsalenko, D. X.-F. Deng, A. Connolly, P. Zhang, E. Yang, C. Watt, Z. Yakhini, A. Ben-Dor, A. Adler, L. Bruhn, P. Tsao, T. Quertermous, E. A. Ashley, Pathway analysis of coronary atherosclerosis, Physiol. Genomics (2005) 00101.2005.

A. Vailaya, P. Bluvas, R. Kincaid, A. Kuchinsky, M. Creech, A. Adler, An architecture for biological information extraction and representation, Bioinformatics 21, 4 (2005) 430.

M. T. Barrett, A. Scheffer, A. Ben-Dor, N. Sampas, D. Lipson, R. Kincaid, P. Tsang, B. Curry, K. Baird, P. S. Meltzer, Z. Yakhini, L. Bruhn, S. Laderman, Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA, Proceedings of the National Academy of Sciences of the United States of America 101, 51 (2004) 17765.

R. Kincaid, VistaClara: an interactive visualization for exploratory analysis of DNA microarrays, Proceedings of the 2004 ACM symposium on Applied computing, ACM Press, Nicosia, Cyprus 2004.

A. Vailaya, P. Bluvas, R. Kincaid, A. Kuchinsky, M. Creech, A. Adler, An architecture for biological information extraction and representation, Proceedings of the 2004 ACM symposium on Applied computing, ACM Press, Nicosia, Cyprus 2004.

Issued Patents

7,750,908 Focus plus context viewing and manipulation of large collections of graphs
7,588,889 Chemical arrays and methods of using the same
7,519,605 Systems, methods and computer readable media for performing a domain-specific metasearch,
and visualizing search results therefrom
7,344,831 Methods for controlling cross-hybridization in analysis of nucleic acid sequences
7,224,362 Systems and methods for providing visualization and network diagrams
7,155,453 Biotechnology information naming system
6,251,588 Method for evaluating oligonucleotide probe sequences
6,461,816 Methods for controlling cross-hybridization in analysis of nucleic acid sequences
6,920,448 Domain specific knowledge-based metasearch system and methods of using
6,950,756 Rearrangement of microarray scan images to form virtual arrays

	Signal Lens: A Focus+Context approach for analyzing large time series of electronic signals. SignalLens enables a very compact visualization which supports ad hoc visual data mining of long electronic time series. A brief video demo was presented by Agilent CTO Darlene Solomon at the IEEE MTT-S International Microwave Symposium in 2009. This work has been accepted for presentation at the 2010 IEEE Information Visualization Conference.
	RFLP Decoder: This software was developed to support authenticating fish species; a problem important to the food industry and critical to complying with new regulations to protect endangered fish species from being overfished. This is now part of an Agilent product (Agilent DNA Fish ID Solution) and was published in the Journal of Visual Experiments. So you can see a complete demo of the lab protocol as well as the software.
	MassVis: This project supported a novel proteomics workflow developed by Kurt Dejgaard at McGill University. A cleverly designed scatter plot interface provides a highly interactive information browser for discovery of putative protein complexes. Pattern similarity matching is used to match ‘‘profiles’’ of similar proteins as a predictor of membership in a protein complex. Both supervised, interactive methods are provided as well as completely unsupervised complex prediction. This work was presented at the 2009 IEEE Symposium on Visual Analytics Science and Technology.
	Line Graph Explorer: A scalable Focus+Context visualization designed specifically for large collections of line graphs. This work was done with the help of Heidi Lam at the University of British Columbia. Presented at AVI 2006, Venice Italy. You can also view a video demo (~100Mb!) LGE was also featured on Information Aesthetics.
	VistaChrom: A visual environment for analyzing array-based comparative genomic hybridization data (aCGH). This was transferred as part of a new commercial aCGH platform and is now part of Agilent Genomic Workbench. See the recent publication in “Information Visualization” for details. Published in Information Visualization. [preprint]
	VistaClara: An exploratory heat map style visualization of gene expression data that combines additional meta-data to assist in finding meaningful patterns and biological insight. Published in SAC 2004 Proceedings.